Re: [gmx-users] grompp gives no molecules were defined in the system

Hi Marysa, The error is about the definition of mulecules, which suggests that there are no [ moleculetype ] directives. Did you #include the proper .itp file(s) with the necessary moleculetype definitions? If not, you'll have to provide more information, probably posting the topology file

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

editing the gro file with PRODRG output. It seems liek PRODRG has modified the co-ordinates that places ligand away from the protein. ~Vivek 2010/1/25 Tsjerk Wassenaar tsje...@gmail.com Hi Vivek, Now when I am processing the modified .gro file to generate box, the ligand and cofactor

Re: [gmx-users] Re: about beta port of C27 FF to gromacs

Hi, --- Program pdb2gmx, VERSION 4.0.7 Source code file: resall.c, line: 344 Fatal error: in .rtp file in residue cmap at line:       -C      N       CA      C       +N :q! --- Did

Re: [gmx-users] Re: about beta port of C27 FF to gromacs

Hi Pär, I actually refered to the .rtp file. I think that the edit was there. Cheers, Tsjerk On Mon, Jan 25, 2010 at 12:24 PM, Pär Bjelkmar bjelk...@cbr.su.se wrote: Hi, --- Program pdb2gmx, VERSION 4.0.7 Source code file: resall.c, line:

Re: [gmx-users] running unrestrained MD for tutorial

Hi David, Always check which version a tutorial is written for. And also always mention which version you're running when posting a question/issue to the list. Now, with this error, I know you're running the (broken) GMX 3.3.2. The tutorial was written for 3.3.1, but will also work with 3.3.3.

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

Hi Vivek, Now when I am processing the modified .gro file to generate box, the ligand and cofactor are going away from the protein molecule and I am not able to analyze the complex. Gradually going away, or suddenly jumping? In the latter case, read up on periodic boundary conditions.

Re: [gmx-users] GMXRC Problem

Hi Pawan, Check which shell you're actually running (probably bash), and source the shell specific GMXRC file (GMXRC.bash). Cheers, Tsjerk On Mon, Jan 25, 2010 at 8:19 AM, pawan raghav pwnr...@gmail.com wrote: Dear Justin, I have some problem regarding GMXRC execution, I got an error while

Re: [gmx-users] Lipid parameters for GROMOS96 force fields

Hi, Well, we have compared the G53a5/6 force field with the 43a2 one and found consistently larger radii of gyration and higher RMSDs, suggesting decreased stability. There's a thorough account of it in my thesis

Re: [gmx-users] how to analysis crystal structure and 2D projections by PCA?

Xi Zhao, Find some elementary text on PCA and read it thoroughly. Tsjerk On Wed, Jan 20, 2010 at 2:40 PM, xi zhao zhaoxiitc2...@yahoo.com.cn wrote: Dear users: I want to analyse a crystal structure by PCA, and want to show its 2D projection, but I meet errors segment fault my procedure:

Re: [gmx-users] dynamic cross correlation map (DCCM)

Hi, Well I'd say that 'DCCM' refers to the matrix (map) of correlations and not to that of covariances. More specifically, it refers to correlations of positional fluctuations. PCA, on the other hand, refers to the extraction of components or axes which better describe the data than the original

Re: [gmx-users] occupancy

Hi Carla, You can do lots of things. You can edit the occupancy field by hand, or do it with a tool like sed. You can also neglect the warning, provided that you're pretty sure the structure is okay. Partial occupancies occur when atoms can not be exclusively assigned to a single position. In

Re: [gmx-users] Missing Residues are list ind pdb file

Hi Jack, On Fri, Jan 15, 2010 at 8:05 PM, Jack Shultz j...@drugdiscoveryathome.com wrote: I'm trying to prep Fe-Hydrogenase again (1YQW). I took out all the non-standard residues. Re-named n-terminal and c-terminal residues. Took out connects because that worked last time though I'm uncertain

Re: [gmx-users] The size of the domain decomposition grid (1) does not match the number of nodes (8).

Hi Chris, Don't have an answer too this one, but noticed the argument to the -np option -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') Maybe it's a bit easier on the eye to use: -np $(sed -n $= $PBS_NODEFILE) Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal

Re: [gmx-users] Unstable Minimizations

On Thu, Jan 14, 2010 at 9:23 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Tsjerk Wassenaar skrev: Hi Jack, On Thu, Jan 14, 2010 at 5:41 PM, Jack Shultz j...@drugdiscoveryathome.com mailto:j...@drugdiscoveryathome.com wrote:    Problem Solved.        I replaced HETATM with ATOM, I fixed

Re: [gmx-users] Unstable Minimizations

Hi Jack, On Thu, Jan 14, 2010 at 5:41 PM, Jack Shultz j...@drugdiscoveryathome.comwrote: Problem Solved. I replaced HETATM with ATOM, I fixed BOTH N-terminal and C-terminal. I kept TER and END. Removed all CONECT. Renamed the CYS to CYS2. No other non-AminoAcid residues were present. Most

Re: [gmx-users] Unstable Minimizations

Hi Jack, Justin, Is this related to last weeks post? I suggested that you might have seen long bond warnings, which in this case certainly show up. Lots of them. But one stands out: there's a break in the chain of 3.3 nm! During minimization an attempt is made to bring these ends together, which

Re: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 = Simulation Broke

Hi Chih-Ying, Like Mark said, start from scratch and trace your steps carefully. There's nothing special about that lysozyme structure. In fact, the protocols I use for the tutorials work flawlessly with it! I think you'd best step through the tutorial again, using 6LYZ.pdb. I know that at some

Re: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 = Simulation Broken

Now try hard to resist running on multiple processors... Tsjerk On Mon, Jan 11, 2010 at 8:11 PM, Chih-Ying Lin chihying2...@gmail.com wrote: Today's Topics:   1. 6LYZ.pdb + Gromacs version 4.0.5 = Simulation Broken      (Chih-Ying Lin)   2. 6LYZ.pdb + Gromacs version 4.0.5 = Simulation

Re: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 = Simulation Broken

Hi Lin, First of all, I would suggest sticking to a single processor until you have a protocol that works. Previously you had an issue with the addition of ions to your .top file. In your protocol, it's not mentioned. Have you made sure that issue is cleared? Cheers, Tsjerk On Sun, Jan 10,

Re: [gmx-users] Opening .o files

Lum, There is none. These are binary object files resulting from compilation of the source code. Why do you think you would need to read those? Tsjerk On Fri, Jan 8, 2010 at 7:06 PM, Lum Nforbi lumngwe...@gmail.com wrote: Dear all,    I am having problems opening the g_energy.o file in the

Re: [gmx-users] Energy units

Hi, I think that the best interpretation is that the energy is given as kJ per mole of simulation systems :) Cheers, Tsjerk On Thu, Jan 7, 2010 at 8:42 AM, Mark Abraham mark.abra...@anu.edu.au wrote: Cheong Wee Loong, Daniel wrote: Thanks Mark for your reply. So if I understand you

Re: [gmx-users] trouble minimizing structure with mdrun

Hi Jack, On Mon, Jan 4, 2010 at 2:44 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Jack, snip After preparation with (V|NA)MD, did pdb2gmx correctly assign chains, or did it tie chains together? In the latter case it would have issued a number of Long Bond Warnings. Did anything else

Re: [gmx-users] Simulation Box break into 16 domains = .tpr file is wrong (Gromacs 3.3.3)

Hi, Tsjerk gave me suggestion to check the .tpr file created by the command grompp. I also suggested to try and find out why the water molecules got garbled. Between adding solvent and energy minimization, you also added chloride to counter the net positive charge. I assume you used genion

Re: [gmx-users] trouble minimizing structure with mdrun

Hi Jack, Can you be more specific? A quick glance at 1YQW shows that there's quite a bit of exotic stuff, including several times the infamous Fe4S4 center. How did you deal with that? At first instance, what protocol did you used, and what error did you get (and at which point)? After

Re: [gmx-users] About gromacs run...

Hi Henry, Doing so will give you a loss of precision and you won't have continuity for the thermo/barostat. You would be better off using tpbconv -extend or tpbconv -until, with the .tpr, .edr, and .trr as input. That will also save editing files. Hope it helps, Tsjerk On Sat, Jan 2, 2010 at

Re: [gmx-users] get 3 roation angles over time

Hi Marc, Which rotation angles? I suppose you mean the Euler angles, but then, XYZ, XYX, ZYZ? I may be able to help. Contact me off list if you're interested. Cheers, Tsjerk On Fri, Jan 1, 2010 at 9:02 AM, marc.spen...@gmx.net wrote: Dear Gromacs users, my system consists of two rigid

Re: [gmx-users] Simulation Break = Due to bad domain decomposition ? (MPI) = Gromacs Version 3.3.3

Hi Lin, I used Gromacs version 3.3.3. There is no domain decomposition in gromacs 3.3.3. Furthermore, you again give no account of what you're doing in terms of command lines and don't show the grompp output. This is pointless. Tsjerk My simulation system = one protein + 20 ligand + water

Re: [gmx-users] LINCS WARNING max 597108032.000000 (between atoms 366 and 368) ?

Hi, So many posts and replies on a single issue, and still no exact command lines, nor grompp output, nor gromacs version. Lin, please be aware that such errors only make sense in the context of what you did. You'll have to provide all information that might be related to it. I'm pretty sure that

Re: [gmx-users] fix a group in truncated octahedron

Wende, This is the third time you post this exact message. Apparently, nobody felt equipped to reply to your post, either because nobody knows the answer, or your message and intent were not clear enough. In either case, reposting your message over and over is completely useless and annoying.

Re: [gmx-users] convert B-factor

Hi Antonio, You can do something like: grep -v ^#@ rmsf1.xvg rmsf1.dat grep -v ^#@ rmsf2.xvg rmsf2.dat paste rmsf1.dat rmsf2.dat | awk '{print $4-$2}' difference.dat That will give you a file with the rmsf difference. You can use editconf to read such data into the b-factor field, although

Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

wrote: Dear Mr Tsjerk Wassenaar : Thank you for your help! I only study on conformation transfromation (transformation) of protein, and need point to corresponding conformation in 2d projection or free energy landscape! I have no any script, please help me! Best regards! [image: 4]http

[gmx-users] Re: Help with Gromacs

assume that the simulation is reliably moving forward? The trajectories at this time are too small to notice any jumps. Pavan On Tue, Dec 22, 2009 at 9:05 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Pavan, The first thing is to formulate your research question. Second you have

Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

closest to that point, by taking the Euclidean distance between the projection and the minimum. You'll have to do a bit of scripting there. Cheers, Tsjerk On Mon, Dec 21, 2009 at 2:51 PM, xi zhao zhaoxiitc2...@yahoo.com.cn wrote: Dear Mr *Tsjerk Wassenaar ：* *Thank you for your help! * *what

Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

Ni hao, Since it's a projection, there is not (in general) a single conformation for each point in the 2D plane. On the other hand, the points you obtained are derived from distinct (ordered) conformations, so it is trivial to retrieve them. Each conformation (time) yields one point: find the

Re: [gmx-users] trjcat error

Hi Anirban, Check each trajectory with gmxcheck to see whether they are okay. Cheers, Tsjerk On Fri, Dec 18, 2009 at 7:32 AM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi ALL, I have 3 5 nano-seconds trajectory files (.trr) of a protein+lipid+water simulation. I am using trjcat to

Re: [gmx-users] g_rms (rmsd vs residue no)

Hi Leila, There is no such option. This has been discussed on the list quite recently. You can try to be creative with index groups to get what you want. Cheers, Tsjerk On Wed, Dec 9, 2009 at 9:56 AM, leila karami karami.lei...@gmail.com wrote: Hi g_rms gives us a xvg file containing rmsd

Re: [gmx-users] g_mindist after trjconv -fit give different results

Hi Elad, You can't count on operations that involve PBC after fitting. In your case, you can use trjconv -fit translation to remove translational degrees of freedom only, keeping the system consistent with PBC. Hope it helps, Tsjerk On Sun, Dec 6, 2009 at 8:50 PM, el...@post.tau.ac.il

Re: [gmx-users] minimum residue distances

Hi Carla, Please be specific with your questions, regardless of your level of expertise and field. Are you after a program to calculate minimal distances, which would be a Gromacs specific question? In that case have a look at g_mdmat, g_mindist, g_dist. Also be sure to get current on the use of

Re: SV: SV: SV: [gmx-users] g_saltbr

Hi, Of course the real answer is in the code... if (bSep) { snew(buf,256); for(i=0; (incg); i++) for(j=i+1; (jncg); j++) { if (nWithin[i][j]) { sprintf(buf,sb-%s:%s.xvg,cg[i].label,cg[j].label); fp=xvgropen(buf,buf,Time (ps),Distance (nm)); ... So, a

Re: SV: SV: SV: [gmx-users] g_saltbr

file a bug report or are you doing it since you understand the code? Thank you all! Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Tsjerk Wassenaar Sendt: on 02-12-2009 19:29 Til: jalem...@vt.edu; Discussion list for GROMACS users Emne: Re: SV: SV

Re: [gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

Hi Daniel, The problem is likely that your vesicle is interacting with itself over the periodic boundaries. There are regions where there is no solvent inbetween. That means that lipids can go over from one image to the other by diffusion, which will not be compensated by using -pbc nojump. You

Re: [gmx-users] g_mindist , trajectory only CA atoms, to small values?

Hi Peter, Instead of the pairs with the shortest distance a much further pair is selected. Although the output pair from atm-pair.out has a distance of more then 100 Angstrom the value in  the file mindist.xvg is smaller then one Angstrom. Periodic Boundary Conditions? You mention in

Re: [gmx-users] Problem with output structures generated by energy minimization with GROMACS 4

Ni Hao, You don't give too much information here. What exactly are you doing? What are the commands? What's the difference between the first and the second pass of EM? One thing to check is whether the output/input file has a correct box definition. Cheers, Tsjerk 2009/11/30 HAO JIANG

Re: [gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

Hi Daniel, If the structure is correct in the coordinate file you used as input to generate the .tpr, you can use that structure as reference to trjconv, using -pbc nojump. Cheers, Tsjerk On Mon, Nov 30, 2009 at 6:17 PM, Daniel Parton daniel.par...@bioch.ox.ac.uk wrote: Hi, Thanks for the

Re: [gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

Hi, trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster You might want to use -dump to extract a specific frame, rather than using -e: trjconv -f a.xtc -o a_cluster.gro -pbc cluster -dump 0 Also, do mind that for a subsequent call to trjconv, using -pbc nojump and the extracted frame as

Re: [gmx-users] Unexpected behavior of g_msd

Hi Darrell, You can check whether the output is identical to a trajectory of the specified frames... It may well be that the counting for the regression is done on the frames read: 100 - 60 = 40 ps Then 4 and 35.9 would correspond to 64 and 95.9. The answer is in the code... But using a

Re: [gmx-users] g_msd = The MSD and periodic boundary condition

Hi, Removing periodicity from the trajectory can be done after simulation using g_traj with the -nojump option. Actually, trjconv -pbc nojump Cheers, Tsjerk Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com -- gmx-users mailing list    gmx-us...@gromacs.org

Re: [gmx-users] covariance

Hi Morteza, Your question suggests a lack of understanding of the principles (not principals) of covariance analysis. It is probably best to read a bit more on the background of this technique, until you realize what it is, what it can do, and what it can't. There are a number of discussions

Re: [gmx-users] pdb2gmx : treat CL as C

Justin, What is the problem?  It looks like you got everything to work, but the .pdb file you've posted is misformatted on the CL lines: ATOM     14  C14 PCD     1      -2.372  -1.395   0.000  1.00  0.00 C ATOM     15 CL1  PCD     1       5.070   1.618  -0.001  1.00  0.00  CL Note how

Re: [gmx-users] pdb2gmx : treat CL as C

Oops, there's an .rtp entry. Shame on me :$ Maybe a good idea though to post the output of pdb2gmx. Cheers, Tsjerk On Tue, Nov 17, 2009 at 3:44 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Justin, What is the problem?  It looks like you got everything to work, but the .pdb file you've

Re: [gmx-users] segmentation fault in g_anaeig

Hi Nilu, Can you paste the exact commands you entered, and indicate the selections you made? Oh, and can you check the archives to whether this is the same problem that was reported a few weeks ago? Cheers, Tsjerk On Tue, Nov 17, 2009 at 5:53 PM, Nilu Chakrabarti nilu.chakraba...@gmail.com

Re: [gmx-users] Segfaults with trjconv and g_dist

Hi Ondrej, This is not a bug, but arises from the inconsistency of the .tpr file and the .xtc file. g_dist uses an internal index group derived from the .tpr file. But that file contains more atoms than the trajectory file, and some index numbers for counterions are higher than the highest entry

Re: [gmx-users] Segfaults with trjconv and g_dist

, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Ondrej, This is not a bug, but arises from the inconsistency of the .tpr file and the .xtc file. g_dist uses an internal index group derived from the .tpr file. But that file contains more atoms than the trajectory file, and some index numbers

Re: [gmx-users] energy minimization - not converge

Hi Leila, Where does it say that you encountered an error? You also could've checked the wiki/mailing lists for this and found that this is normal and sufficient for starting an MD simulation. Cheers, Tsjerk On Wed, Nov 11, 2009 at 9:10 AM, leila karami karami.lei...@gmail.com wrote: Hi I

Re: [gmx-users] pdb2gmx -missing

Hi, Well, -ignh is not the right answer here. I recall that just a few days ago someone posted the same problem. For Amber you need to tag the first and last residue. For your GLY, it means you have to rename it to NGLY. Itamar, The warning mentions an atom missing from the .pdb file. These

Re: [gmx-users] Constraints Restraints

Hi Darrell, Constraints and restraints also apply to relative positions. A bond constraint fixes the bond to a certain distance. constraints = all-bonds means that all bonds are to be converted to constraints, rather than have them flexible, e.g. harmonic. Harmonic bonds are actually more like

Re: [gmx-users] Re: Installation on Windows

Hi Pawan, It may be unintentional, but your post is rather impolite. Do mind that the people that answer questions here have no obligation to help you. Nobody should put any effort in making something more user friendly, unless it is part of their job, e.g. for classes. You can ask if somebody

Re: [gmx-users] topology file in .dat format

Hi Subarna, There is no .dat format for topologies. It may be named .dat, but the inside (format) is what matters. If you're confident it is gromos96 format, you can #include it the same way as other molecule definition topology files. Do mind that there's quite a difference between GROMOS96

Re: [gmx-users] NAN in g_anaeig -proj

Hi Alex, Sorry for not replying earlier. Still haven't had time to do checks myself. But have you already tried to see what happens if you only request projections?: g_anaeig_d -v sss_1000_eigenvec.trr -f sss_mdsi_1000.trr -s sss_mdsi_1000.tpr -first 1 -last 1 -n sss.ndx -proj Cheers, Tsjerk

Re: [gmx-users] Re: NAN in g_anaeig -proj

: 6 Date: Fri, 30 Oct 2009 12:53:28 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] NAN in g_anaeig -proj To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 8ff898150910300453n550a6358sf596cff4771c9...@mail.gmail.com Content-Type: text/plain; charset

Re: [gmx-users] nans in g_anaeig

Hi Alex, Can you paste the actual sequence of commands you used? Cheers, Tsjerk 2009/10/27 alexander yakovenko yakovenk...@ukr.net: Hi all! I run into a problem trying to project trajectory on the eigenvector(s) (with g_anaeig -proj ) from covariace matrix - all projections are nan. The

Re: [gmx-users] Box vector error

Hi Prem, There is just something terribly wrong with your system if it goes flat like that. But with only the information you give here, no one can tell you more than that. Cheers, Tsjerk On Wed, Oct 21, 2009 at 10:18 AM, Prem Singh Kaushal p...@mbu.iisc.ernet.in wrote: Dear All     I am

Re: [gmx-users] Re: how to calculate g_sdf and ionic conductivity

Hi IMA, Have you checked the g_sdf help? It provides information about the purpose of the four groups, and how they should be related. What you're trying to do here is nonsensical. Do you know what you want to do (physicochemically)? Cheers, Tsjerk On Wed, Oct 21, 2009 at 11:15 AM, naimah

Re: [gmx-users] Long Simulation Time

Hi Lin, That is likely related to running with a scheduler that only allows a limited time for processes (the wall time). Under 'normal' conditions the simulation will not break due to long running times. It may break due to a full disk, which can be related to a long running time :p Cheers,

Re: [gmx-users] protein domain separate

Hi, You have to use -pbc nojump with a _suitable_ reference. Cheers, Tsjerk On Sun, Oct 18, 2009 at 11:59 AM, hazizian haziz...@razi.tums.ac.ir wrote: Hi again I use -pbc mol -ur compact but the problem still exist. -- Tehran University of Medical Sciences www.tums.ac.ir -- This

Re: [gmx-users] Example file for DNA

Hi, I stripped the following from a script of mine. The original script did some additional things before, involving first a conversion from PDB to CNS format and later to GMX format. I rearranged it without testing. You can try it and if you find that it doesn't do a proper job, you can send me

Re: [gmx-users] Water molecule starting at atom X can not be settled; can't find a solution

Hi Simone, The temperature coupling might be a cause for an error like that to occur. Try to understand that coupling ions separately may cause large fluctuations in there velocities and hence cause sudden large displacements that may put an ion on top of a solvent molecule that can't be settled

Re: [gmx-users] Re: Re: Pyroglutamic Acid - Topology (pdb2gmx)

Hey, The problem comes from the special linkage between PGL and whatever the subsequent amino acid is - the amide is formed through the side chain.  As such, you will need to specify a special bond in specbond.dat before this connectivity will be recognized.  If this is successful, then the

Re: [gmx-users] g_hbond and hydrogen bonds involving sulfur

Hi Diana, Well, minorities should not be disregarded just because they are poorly represented...In some cases a rare event makes all the difference. I think it would be helpeful to have the possiblity to calculate S-H...X bonds or X-H...S bonds with g_hbond. In many cases these tools come

Re: [gmx-users] forcefield

Hi Lalitha, Zebularine is beyond the trivial. You may be able to derive something reasonable from the other bases using 'chemical intuition' (cytidine, thymidine, uracil), but it's likely that the electronic structure of the ring is too different to justify an approach like that. Likely you

Re: [gmx-users] run g_cover in parallel

Hi, I wonder if there a way to run g_cover in paralel in order to make things run faster? No. Obviously you can use -dt to reduce the number of frames you analyze. In most cases it's not the reading of frames, but the diagonalization of the covariance matrix that consumes most of the time.

Re: Re: [gmx-users] RMSF reference state?

Hi Pan Wu, There are two things to distinguish: 1. The reference structure used to remove translational and rotational degrees of freedom 2. The reference against which the deviations (on a per atom base) are calculated that are then squared, averaged and taken the root of (root mean square

Re: [gmx-users] RMSF reference state?

Hi, Actually, Justin is completely right (and I should've checked g_rmsf -h). -od calculates the RMSD from the structure in the frame against the structure in the topology file. This does not nullify the statements regarding references for fitting and references for deviations though :p Cheers,

Re: [gmx-users] Advantage of NPT over NVT?

Hi, In addition to the remarks of Ran and Mark, also note that with NVT the density of your system may change significantly and artificially, relating to changes in your protein. This in turn affects the dynamics of your protein, which should be considered an artefact of NVT simulations. Cheers,

Re: [gmx-users] Question about genion, error happens

Hi Pan Wu, You use -pname to specify that the added sodium ions should have the name 'Na'. Accordingly, at the end of your .top file genion writes a line under [ System ] specifying the number of 'Na' molecules. But that requires that 'Na' is defined, which is not the case, given the error. The

Re: [gmx-users] pdb2gmx problem

Hi Abhijit, I think the Zinc ion goes with chain B and uses the same identifier. Given the fact that you didn't quite understand the error, and found it necessary to post a question, this raises another question: should you be wanting to simulate a protein with a zinc ion?

Re: [gmx-users] Making Commands Non-Interactive

Cool. You can also write a python script to generate and execute your C-code, which you then wrap with Java to be executed through Ruby... etc. Erik, can you maybe give the assembly solution? :p Tsjerk On Mon, Oct 5, 2009 at 10:15 AM, Alexander Bujotzek bujot...@zib.de wrote: I once wrote some

Re: [gmx-users] Making Commands Non-Interactive

Hi, Is trjconv parallelizable?  This is nowhere in the documentation, but if it is, that would be very interesting... Well, the most interesting part in that regard is probably the I/O. But that's the hardest bit to parallelize. How to pass the choice 0 in the script Just as you would on

Re: [gmx-users] Re: a naive question on restraints and constraints

Hi, It's actually a bit more nuanced and the use of these idioms is not really backed by a semantic distinction: In Gromacs, a constraint fixes some property to a value, whereas a restraint penalizes deviation of a property from a certain value. Cheers, Tsjerk On Wed, Sep 30, 2009 at 2:03 AM,

Re: [gmx-users] water molecule cannot be settled

Hi Carla, You may have a water molecule trapped inside your protein. Check the water molecule with the given atom number in a viewer, together with your structure. If it is inside, you can try to remove it manually from the system, editing the structure file and decreasing the amount of solvent

Re: [gmx-users] Generating a .gro file from .pdb file

Hi, No, that procedure generates a topology file, it is not the correct tool for a change of coordinate format (which is almost never needed anyway). As a side effect, it regularizes an input coordinate file which might have been in one of various formats, and outputs a coordinate file whose

Re: [gmx-users] Trjconv trouble

Hi Guy, Which version are you using? It may be there's a flaw in the code. If you want the forces in human readable format, you can also try converting the .trr to .g96 Hope it helps, Tsjerk On Mon, Sep 28, 2009 at 9:59 PM, Vigers, Guy guy.vig...@arraybiopharma.com wrote: Dear Gromacs users,

Re: [gmx-users] Probelm of g_rms

Hi Nikhil, Try extracting the frame just before and just after the jump and view them in pymol/vmd/rasmol/... to check for a possible cause. Cheers, Tsjerk On Fri, Sep 25, 2009 at 5:50 AM, nikhil damle pdnik...@yahoo.co.in wrote: Yes. I am correcting the trajectory for periodicity Regards,

Re: [gmx-users] Can Gromacs produce the data from NMR?

Hi Lin, You should check the manual, check the literature on cross validation of MD/NMR, and note that the tutorial you've been following has two items related to it, namely distance analysis, including NOE back calculation, and calculation of order parameters. Hope it helps, Tsjerk On Fri,

Re: [gmx-users] editconf and g_rmsdist

Hi Soren,  Why I am seeing this difference? Is it due to round-off’s after the transformation to center the molecule in the box? Or am I using g_rmsdist wrongly? It's a bit weird indeed. You might be right that it's due to round-off errors. You can try to copy the original gro file and

Re: [gmx-users] Periodic Boundary Conditions Location of Atoms Near Box Edges

Hi Darrell, No, you just have to make sure that the bond lengths are correct in the periodic system. The PBC are invariant under translation. Cheers, Tsjerk On 9/17/09, Darrell Koskinen darre...@ece.ubc.ca wrote: Dear GROMACS Gurus, In order to correctly model an infinite graphene sheet

Re: [gmx-users] Re: System has non-zero total charge: 2.570000e+00

Hi, On Sun, Sep 13, 2009 at 8:55 AM, Vitaly V. Chaban vvcha...@gmail.com wrote: before energy minimization step , I performed the preprosessing step using grompp  . However, there’s a note that : System has non-zero total charge: 2.57e+00 “. why the total charge of system is not an

Re: [gmx-users] bypassing pdb2gmx

Hi Amit, You don't need to convert the .pdb file. Gromacs can handle several file formats, including .pdb. If you have a topology that matches the .pdb in terms of atoms, then you can simply proceed with the subsequent steps. pdb2gmx is not exactly meant to convert the structure file to another

Re: [gmx-users] how to use a new force field

Hi, Well, to *add* a new force field, summerizing and extending the replies given earlier, you edit the file FF.dat in the directory $GMXPATH/share/gromacs/top.This file looks like 11 ffG43a1 GROMOS96 43a1 force field ffG43b1 GROMOS96 43b1 vacuum force field ffG43a2 GROMOS96 43a2 force field

Re: [gmx-users] LINCS

Hi, .snip... No, because that's not a well-defined proposition. You could generate a small box with one solute +solvent, and then use *genbox* to replicate it. genconf, rather than genbox: genconf -f in.gro -o out.gro -nbox nx ny nz with suitable nx, ny and nz for nx*ny*nz copies.

Re: [gmx-users] grompp.mdp

Hi kayal, Well, given that it reads Fatal error your final question seems a bit odd, doesn't it? How did you obtain the topology? Apparently, there's a bit more specified in it than a single butane! Besides, I notice that you use the GROMOS force field, which is a united atom force field. That

Re: [gmx-users] cluster graph

Hey, According to the urban dictionary: II. Defining 'Noob' Contrary to the belief of many, a noob/n00b and a newbie/newb are not the same thing. Newbs are those who are new to some task* and are very beginner at it, possibly a little overconfident about it, but they are willing to learn and fix

Re: [gmx-users] Control Atoms for Hydroxide ?

Hi, Well, who'd need control atoms? You'd just need to position it at a certain distance along a random vector. If you're talking about it as part of a water cluster or something, technically speaking it's not a hydroxide anymore :) On another note, as I mentioned before, the proton has an

[gmx-users] Re: solvation

Hi, Right, but genbox puts things inside the rectangular brick corresponding to the unit cell, starting at the origin. That means that if the solute is on one end, then placing something close to the part that sticks out will actually be put on the other side of the box. But maybe I just want to

Re: [gmx-users] How to start the Normal Modes Analysis?

Hi, Start out with reading and only stop reading when you grasp what it is, what it does, what it can do and what it can't do. Tsjerk On Thu, Aug 13, 2009 at 10:37 PM, Justin A. Lemkuljalem...@vt.edu wrote: Chih-Ying Lin wrote: Hi I read the Manual and still have no idea about the Normal

Re: [gmx-users] minimization

Hi Morteza, How did you obtain these structures? If they were modeled, maybe in part, check for knots and chain overlaps. Also check whether you're using PBC and if so, whether the box is large enough or you may have overlapping periodic images. Cheers, Tsjerk 2009/8/13 Mark Abraham

Re: [gmx-users] minimization

Hmm, was the OPLSAA run following the GMX one on the dimer or also performed on the monomers? If you feed a multimeric protein without chain identifiers (like in a .gro file) to pdb2gmx, it will bind the different chains together. That would be a good cause for a crash. So I'd say check that

Re: [gmx-users] Re: solvation

Hi, Thanks for the answer. When I said far away means my pore was in one corner of vmd window and the water molecules in opposite corner (almost). Did I miss something or did neither Vitaly nor Justin reply Are you perhaps seeing the effect of periodic boundary conditions?. Tsjerk -- Tsjerk

Re: [gmx-users] minimization

Hi Morteza, I think it will be best for all of us if you can provide the exact command lines you are using, and the output of pdb2gmx for the well-performing and an ill-performing force field. Otherwise I'm afraid that we will not be able to get any further than making guesses. Cheers, Tsjerk

Re: [gmx-users] energy minimization

Hi, On Wed, Aug 12, 2009 at 3:06 AM, Mark Abrahammark.abra...@anu.edu.au wrote: Jamie Seyed wrote: Dear all, I performed an md simulation but it crashed at the beginning because according to it system was exploding. Also when I tried to see the system by ngmx, there was no water anymore

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